As well as redundancies, Hawke's Bay Today has been told the restructure has led to uncertainty amongst staff, low-morale at council, and the resignations of a number of experienced staff.
A staff member affected by the restructure said the "true agenda" of the council's top management had led to "countless years of experience being shown the door".
"The new top management appears to regard long, faithful service as a sign of weakness," they said. "Now the one-team spirit, that served the ratepayers so well, has been dispensed with - leaving many staff feeling unsupported and undervalued.
"Morale is at an all-time low and sadly, some are leaving of their own volition just to get out of the place."
Mr Jack and Napier mayor Bill Dalton both said that although significant changes like the restructure would impact staff morale, they were working through it as quickly as possible.
The mayor said although "the easy thing to do, would be to do nothing", in the interest of ratepayers the restructure was being undertaken to increase efficiency.
While it created some temporary loss of morale, and uncertainty, he believed when the process was complete the council would have a better, and more efficient structure.
"And then we will work on getting everybody's morale back up top."
Mr Jack said it was expected that there would be a "small pocket of people" not engaged, "but there are lots of people who are extremely supportive and engaged in the direction of council."
Another staff member claimed the low morale meant there were "many long-serving, loyal staff with years of experience, knowledge and expertise walking out the door in disgust."
These resignations of "talented and experienced" people was among the "disastrous" results of the restructure, the Napier City Council Staff Association said.
Mr Jack said he could not comment on staff leaving by choice.
Speaking on the association's behalf, lawyer Bill Calver claimed the changes were having an impact on the council's service delivery, and creating uncertainty amongst staff.
"People just don't know whether they're going or staying," he said.
Mr Jack disputed any negative impact on service delivery, and said staff were very clear if their position would be affected.
"There's been a lot of communication with the staff through this whole process," he said. He added that staff had been engaged through briefings, and were kept informed of the changes which were occurring.
Those impacted were given support, and advice.
Currently the council was still in a transition period, including recruitment and selection for new roles under the realigned structure.
Existing staff were also being given the opportunity to apply for roles, and council was looking at redeploying them.
He expected the process to continue until at least the end of this year.